nt2py 1.2.0

Post-processing & visualization toolkit for the Entity PIC code

nt2.py

Python package for visualization and post-processing of the Entity simulation data. For usage, please refer to the documentation. The package is distributed via PyPI:

pip install nt2py

Usage

Simply pass the location to the data when initializing the main Data object:

import nt2

data = nt2.Data("path/to/data")
# example: 
#   data = nt2.Data("path/to/shock")

The data is stored in specialized containers which can be accessed via corresponding attributes:

data.fields     # < xr.Dataset
data.particles  # < dict[int : xr.Dataset]
data.spectra    # < xr.Dataset

If using Jupyter notebook, you can quickly preview the loaded metadata by simply running a cell with just data in it (or in regular python, by doing print(data)).

Examples

Plot a field (in cartesian space) at a specific time (or output step):

data.fields.Ex.sel(t=10.0, method="nearest").plot() # time ~ 10
data.fields.Ex.isel(t=5).plot()                     # output step = 5

Plot a slice or time-averaged field quantities:

data.fields.Bz.mean("t").plot()
data.fields.Bz.sel(t=10.0, x=0.5, method="nearest").plot()

Plot in spherical coordinates (+ combine several fields):

e_dot_b = (data.fields.Er * data.fields.Br +\
           data.fields.Eth * data.fields.Bth +\
           data.fields.Eph * data.fields.Bph)
bsqr = data.fields.Br**2 + data.fields.Bth**2 + data.fields.Bph**2
# only plot radial extent of up to 10
(e_dot_b / bsqr).sel(t=50.0, method="nearest").sel(r=slice(None, 10)).polar.pcolor()

You can also quickly plot the fields at a specific time using the handy .inspect accessor:

data.fields\
    .sel(t=3.0, method="nearest")\
    .sel(x=slice(-0.2, 0.2))\
    .inspect.plot(only_fields=["E", "B"])
# Hint: use `<...>.plot?` to see all options

Or if no time is specified, it will create a quick movie (need to also provide a name in that case):

data.fields\
    .sel(x=slice(-0.2, 0.2))\
    .inspect.plot(name="inspect", only_fields=["E", "B", "N"])

You can also create a movie of a single field quantity (can be custom):

(data.fields.Ex * data.fields.Bx).sel(x=slice(None, 0.2)).movie.plot(name="ExBx", vmin=-0.01, vmax=0.01, cmap="BrBG")

For particles, one can also make 2D phase-space plots:

data.particles[1].sel(t=1.0, method="nearest").particles.phaseplot(x="x", y="uy", xnbins=100, ynbins=200, xlims=(0, 100), cmap="inferno")

You may also combine different quantities and plots (e.g., fields & particles) to produce a more customized movie:

def plot(t, data):
    fig, ax = mpl.pyplot.subplots()
    data.fields.Ex.sel(t=t, method="nearest").sel(x=slice(None, 0.2)).plot(
        ax=ax, vmin=-0.001, vmax=0.001, cmap="BrBG"
    )
    for sp in range(1, 3):
        ax.scatter(
            data.particles[sp].sel(t=t, method="nearest").x,
            data.particles[sp].sel(t=t, method="nearest").y,
            c="r" if sp == 1 else "b",
        )
    ax.set_aspect(1)
data.makeMovie(plot)

You may also access the movie-making functionality directly in case you want to use it for other things:

import nt2.export as nt2e

def plot(t):
  ...

#             this will be the array of `t`-s passed to `plot`
#                           |
#                           V
nt2e.makeFrames(plot, np.arange(100), "myAnim")
nt2e.makeMovie(
    input="myAnim/", output="myAnim.mp4", number=5, overwrite=True
)

# or combined together
nt2e.makeFramesAndMovie(
    name="myAnim", plot=plot, times=np.arange(100)
)

Plots for debugging

If the simulation also outputs the ghost cells, nt2py will interpret the fields differently, and instead of reading the physical coordinates, will build the coordinates based on the number of cells (including ghost cells). In particular, instead of, e.g., data.fields.x it will contain data.fields.i1. The data will also contain information about the meshblock decomposition. For instance, if you have Nx meshblocks in the x direction, each having nx cells, the coordinates data.fields.i1 will go from 0 to nx * NX + 2 * NGHOSTS * Nx.

You can overplot both the coordinate grid as well as the active zones of the meshblocks using the following:

ax = plt.gca()
data.fields.Ex.isel(t=ti).plot(ax=ax)
data.plotGrid(ax=ax)
data.plotDomains(ax=ax)

Keep in mind, that by default Entity converts all quantities to tetrad basis (or contravariant in GR) and interpolates to cell centers before outputting (except for the ghost cells). So when doing plots for debugging, make sure to also set as_is = true (together with ghosts = true) in the [output.debug] section of the toml input file. This will ensure the fields are being output as is, with no conversion or interpolation. This does not apply to particle moments, which are never stored in the code and are computed only during the output.

Dashboard

Support for the dask dashboard is still in beta, but you can access it by first launching the dashboard client:

import nt2 
nt2.Dashboard()

This will output the port where the dashboard server is running, e.g., Dashboard: http://127.0.0.1:8787/status. Click on it (or enter in your browser) to open the dashboard.

CLI

Since version 1.0.0, nt2py also offers a command-line interface, accessed via nt2 command. To view all the options, simply run:

nt2 --help

The plotting routine is pretty customizable. For instance, if the data is located in myrun/mysimulation, you can inspect the content of the data structure using:

nt2 show myrun/mysimulation

Or if you want to make a quick plot (a-la inspect discussed above) of the specific quantities, you may simply run:

nt2 plot myrun/mysimulation --fields "E.*;B.*" --isel "t=5" --sel "x=slice(-5, None); z=0.5"

This plots the 6-th snapshot (t=5) of all the E and B field components, sliced for x > -5, and at z = 0.5 (notice, that you can use both --isel and --sel). If instead, you prefer to make a movie, simply do not specify the time:

nt2 plot myrun/mysimulation --fields "E.*;B.*" --sel "x=slice(-5, None); z=0.5"

If you want to only install the CLI, without the library itself, you may do that via pipx: pipx install nt2py.

Features

1. Lazy loading and parallel processing of the simulation data with dask.
2. Context-aware data manipulation with xarray.
3. Parallel plotting and movie generation with multiprocessing and ffmpeg.
4. Command-line interface, the nt2 command, for quick plotting (both movies and snapshots).

Testing

There are unit tests included with the code which also require downloading test data with git lfs (installed separately from git). You may download the data simply by running git lfs pull.

TODO

• Unit tests
• Plugins for other simulation data formats
• Support for sparse arrays for particles via Sparse library
• Command-line interface
• Support for multiple runs
• Interactive regime (hvplot, bokeh, panel)
• Ghost cells support
• Usage examples